The AGRE sample was genotyped on the Illumina HapMap550 array (20), which yields genotypes for roughly 550 000 SNPs of the 1 million contained on the 1M chip. To make these data comparable with the 1M platform, we inferred the missing SNP genotypes by using three sources of information: haplotypes called from trios genotyped on the 1M, haplotypes called from the HapMap550 genotypes and a small set of 105 samples that were genotyped on both platforms and yielded high-quality genotypes. This smaller set of overlapping samples was used to evaluate the accuracy of inferred genotypes. We used Beagle 3.0.1 to call haplotypes and infer missing genotypes (47). Because Beagle 3.0.1 allows only families with a single offspring, we created trios from multiplex families; inferred missing genotypes; then, after putting family data back together, resolved inconsistencies when possible and ‘zeroed’ inconsistencies otherwise. Using the 105 samples genotyped on both platforms, we assessed imputation accuracy; imputed genotypes for an SNP were retained only when none of the called genotypes were discrepant with the 1M genotypes. Following this QC process, each sample from the AGRE data set contained genotypes from the HapMap550 and 248 642 additional imputed genotypes for subsequent analysis.
